Fix saltstack install, remove sudo from devel script

Bioconductor · Jan 23, 2025 · bcf9af8 · bcf9af8
1 parent 0831cbd
commit bcf9af8
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Showing 2 changed files with 28 additions and 26 deletions.
diff --git a/startup_bbs_standalone_devel.sh b/startup_bbs_standalone_devel.sh
@@ -1,53 +1,54 @@
 #!/usr/bin/env bash
 
 # Basic deps
-sudo apt update -qq
-sudo apt -y install curl git build-essential python3 python3-pip locales wget
+apt update -qq
+apt -y install curl git build-essential python3 python3-pip locales wget
 
 # Set up saltstack
 
-# https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/ubuntu.html
+#https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/linux-deb.html
 
-sudo curl -fsSL -o /etc/apt/keyrings/salt-archive-keyring-2023.gpg https://repo.saltproject.io/salt/py3/ubuntu/22.04/amd64/SALT-PROJECT-GPG-PUBKEY-2023.gpg
-echo "deb [signed-by=/etc/apt/keyrings/salt-archive-keyring-2023.gpg arch=amd64] https://repo.saltproject.io/salt/py3/ubuntu/22.04/amd64/latest jammy main" | sudo tee /etc/apt/sources.list.d/salt.list
+mkdir -p /etc/apt/keyrings
+curl -fsSL https://packages.broadcom.com/artifactory/api/security/keypair/SaltProjectKey/public | tee /etc/apt/keyrings/salt-archive-keyring.pgp
+curl -fsSL https://github.com/saltstack/salt-install-guide/releases/latest/download/salt.sources | tee /etc/apt/sources.list.d/salt.sources
 
-sudo apt-get -y update
-sudo apt-get -y install salt-minion
-sudo service salt-minion stop
-sudo systemctl disable salt-minion
+apt-get -y update
+apt-get -y install salt-minion
+service salt-minion stop
+systemctl disable salt-minion
 
 # Assumes the repository has already been cloned to the working directory
 # cd ~
 # git clone -b standalone https://github.com/Bioconductor/bioconductor_salt
 
 # Set up bioconductor's saltstack
-sudo cp -r bioconductor_salt/saltstack/salt /srv
-sudo cp -r bioconductor_salt/saltstack/pillar /srv
-sudo cp bioconductor_salt/saltstack/minion.d/minion.conf /etc/salt/minion
+cp -r bioconductor_salt/saltstack/salt /srv
+cp -r bioconductor_salt/saltstack/pillar /srv
+cp bioconductor_salt/saltstack/minion.d/minion.conf /etc/salt/minion
 
-sudo mv /srv/pillar/custom/devel_standalone.sls /srv/pillar/custom/init.sls
+mv /srv/pillar/custom/devel_standalone.sls /srv/pillar/custom/init.sls
 
-sudo salt-call --local state.highstate || true
+salt-call --local state.highstate || true
 
 # Find R path and check that it works
 if ! /home/biocbuild/bbs-*/R/bin/R --version > /tmp/rver; then exit 1; fi
 
 RPATH="$(echo /home/biocbuild/bbs-*/R/bin)"
 
-echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/profile
-echo "export PATH='$PATH:$RPATH'" | sudo tee -a /etc/bash.bashrc
+echo "export PATH='$PATH:$RPATH'" | tee -a /etc/profile
+echo "export PATH='$PATH:$RPATH'" | tee -a /etc/bash.bashrc
 
-echo "#!/bin/bash" | sudo tee /bbs_r_start
-echo "$RPATH/R \"\$@\"" | sudo tee -a /bbs_r_start
+echo "#!/bin/bash" | tee /bbs_r_start
+echo "$RPATH/R \"\$@\"" | tee -a /bbs_r_start
 
-sudo chown biocbuild /bbs_r_start
-sudo chmod +x /bbs_r_start
+chown biocbuild /bbs_r_start
+chmod +x /bbs_r_start
 
-sudo ln -s /home/biocbuild/bbs-*-bioc/R/bin/R /usr/bin/R
-sudo ln -s /home/biocbuild/bbs-*-bioc/R/bin/Rscript /usr/bin/Rscript
+ln -s /home/biocbuild/bbs-*-bioc/R/bin/R /usr/bin/R
+ln -s /home/biocbuild/bbs-*-bioc/R/bin/Rscript /usr/bin/Rscript
 
 # Cleanup
 # rm -rf /srv /etc/salt
-# sudo apt-get -y purge salt-minion
+# apt-get -y purge salt-minion
 
 
diff --git a/startup_bbs_standalone_release.sh b/startup_bbs_standalone_release.sh
@@ -6,10 +6,11 @@ sudo apt -y install curl git build-essential python3 python3-pip locales wget
 
 # Set up saltstack
 
-# https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/ubuntu.html
+#https://docs.saltproject.io/salt/install-guide/en/latest/topics/install-by-operating-system/linux-deb.html
 
-sudo curl -fsSL -o /etc/apt/keyrings/salt-archive-keyring-2023.gpg https://repo.saltproject.io/salt/py3/ubuntu/22.04/amd64/SALT-PROJECT-GPG-PUBKEY-2023.gpg
-echo "deb [signed-by=/etc/apt/keyrings/salt-archive-keyring-2023.gpg arch=amd64] https://repo.saltproject.io/salt/py3/ubuntu/22.04/amd64/latest jammy main" | sudo tee /etc/apt/sources.list.d/salt.list
+mkdir -p /etc/apt/keyrings
+curl -fsSL https://packages.broadcom.com/artifactory/api/security/keypair/SaltProjectKey/public | sudo tee /etc/apt/keyrings/salt-archive-keyring.pgp
+curl -fsSL https://github.com/saltstack/salt-install-guide/releases/latest/download/salt.sources | sudo tee /etc/apt/sources.list.d/salt.sources
 
 sudo apt-get -y update
 sudo apt-get -y install salt-minion